Clefts of the lip and/or palate (CLP) are common birth defects of complex etiology. About 70% of individuals are born with an isolated cleft and no other structural or cognitive abnormalities. Clefts affect 1 in 700 births and require surgical, nutritional, dental, speech, and behavioral interventions. They impose substantial economic burdens with an expense per person in excess of $200,000 lifetime. In addition to their impact in early life, CLP is associated with a lifetime increase in death from all causes as well as an increased risk for mental health disorders and cancer. It is now practical to identify common variants associated with the etiology of complex traits by using a combination of family collections, careful phenotyping, and genome wide associations studies (GWAS). The next critical step of moving from association to specific causal variant identification has been difficult although there is one success in CLP studies. This next step will be greatly facilitated by deep sequence analysis of the associated regions with subsequent confirmation by expression and functional analysis. We will use a large (1900 case/parent trios) recently completed GWAS coupled to samples and data from 3 smaller, published GWAS studies to select regions for deep sequencing. Four well replicated loci/genes will form the core of this effort (IRF6, MAFB, ABCA4 and 8q24) with two other genes (VAX1 and F0XE1) selected that have compelling supportive data as well. A strong team has been assembled to carry out the work and the project has many novel and innovative features including: parental samples available on 3500 cases enabling use of the transmission disequilibrium test for analysis and the detection of de novo rare variants;a confirmed etiologic variant in IRF6 that provides a "control";close collaborations that allow for expression analysis to be used in both region selection and mutation verification;collaborations to provide functional replication in mouse and fish;the Co-I's leadership of the FaceBase consortium that will provide for rapid dissemination of data and results to the craniofacial community. We believe this project can contribute to an overall better understanding of how to use sequence data to find causal variants and to the causes of CLP. RELEVANCE: Conversion of genome-wide (GWAS) association signals to finding specific mutations is critical to genetic findings into clinical utility. This project will take advantage of a very large GWAS on cleft lip and palate that includes parental samples that provide unique opportunities for detection of causal mutations for this important birth defect. It will provide opportunities for comparative data analysis that will be useful to other studies undergoing similar approaches.